Flux
by I Took the One Less Travelled
Summary: Rose Tyler is a rogue Time Agent with a mission. Jack Harkness one day fell through a rift in the Boeshane and ended up in 21st Century Cardiff. And the Ninth Doctor and his companion, Amy Pond, travel the stars, somewhat concerned about the words 'Bad Wolf' that keep showing up everywhere they turn. Massively AU. Doctor/Rose.
1. Crashing In Leadworth

Leadworth, England, 1996

It was a quiet, tranquil night in the little town of Leadworth, located in England. The date was the third of September, 1996, and seven-year old Amelia Pond was probably the only person that was still awake in the sleepy little town. The girl in question, currently the only occupant of the big old, drafty house, was kneeling next to her bed with her hands in perfect prayer position.

She was disturbed from this by a loud crash coming from her front yard. She leapt to her feet, and, casting an anxious glance at the crack in her wall, hurried down the stairs and out the front door. There was a tall, blue box, laying sideways among the ruins of where her shed used to be.

Amelia examined the box from a distance, keeping caution around the smoldering ruin.

Then the doors popped open from the side, and a grappling hook clanged into place on the bottom of the box. And, as Amelia backed away, still staring, a man popped out. He was wearing an absolutely _shredded_ suit—he looked downright raggedy. He had floppy brown hair, and a slim bit of metal, about the size of a pen, with a blue light affixed onto the end clutched between his teeth.

His chin was sort of prominent, and he was kind of funny-looking, but okay, she decided. He looked at her for a second before grinning delightedly.

"Amy! I mean, Amelia! There you are. People call you Amelia now, don't they? Brilliant name, Amelia Pond. Glad I get to call you that, at least for now."

She was instantly suspicious. "How do you know my name?"

"Oh, right! We haven't met yet, have we? Hello, Amelia, I'm your Raggedy Doctor! I travel all of time and space in my blue box, and you'll get to come with me! When you're a little but older, of course. But for now, I'm here about... what was I here about? I crashed, I didn't mean to come here. But there's something that I'm supposed to do, isn't there? Oh, _right_! There's a scary crack in your wall, and I'm here to fix it. But first, can I have an apple? I'm starving, and I love apples!"

"You can fix the crack?" Amelia asked suspiciously. After all, she had just been asking for someone to come and fix the crack in her wall, and she wasn't about to look a gift horse in the mouth, even if his suit was shredded, and he talked a lot more than most people, and it was sort of weird that he knew her name.

"Yep!"

"Okay. I'll get you an apple, then I'll show you the crack," she agreed, leading the way to the front door. She glanced behind her to check that he was following, and stared in shock as he walked straight into a tree and keeled over on his face. He popped back up moments later.

"New controls," he said. "Steering's still off. How about that apple?"

She got him an apple, and dodged when he hurled it across the room, shrieking about how he hated apples. "I thought you loved them?"

"Ehhh. Nope. Hate apples. New mouth, new rules. Yogurt!"

She got him yogurt. "No, nevermind. Hate yougurt, it's just stuff with bits in it!"

"What's wrong with you?" Amelia demanded, eyeing him suspiciously.

"Me? What's wrong with me? I don't know, what's wrong with you? You're Scottish, fry something! Amy!" He whined. "Oooohh. Still rude. Still not ginger. And you think I'm rude, don't you? You'll get used to it."

So she fried him something. Bacon, in fact. He accused her of trying to poison him. She got him bread and butter, and he threw it at the neighbor's cat. She offered carrots, and he called her crazy. Then he dug fish fingers and custard out of the freezer, cooked it all up, and sat down with it contentedly. Amelia helped herself to the ice cream, feeling that she was due something good, and it wasn't like Aunt Sharon would even notice, right?

"So, why haven't your parents woken up yet?"

"Don't have parents," Amelia said, shrugging. "Just an aunt."

"I don't even have an aunt," the Doctor said.

"You're lucky."

"I know," he agreed, leaning forward like he was sharing a secret. "Your aunt, then. Why haven't we woken her with all of the noise we've made?"

"She's not here. She went into London for a few days."

"She left you all alone?"

"I'm not scared," Amelia protested defensively, crossing her arms.

"Oh, I should think not," the Doctor assured her. "Box falls out of the sky, man falls out of the box, man knows your name when you've never seen him before, man eats fish custard, and look at you—just sitting there. You know what I think?"

"What?"

"Must be a hell of a scary crack in your wall."

**So, there are several things that you might be thinking right now. First—the summary said that this fic was about Nine and Rose, why are we seeing Amy and Eleven? Did you publish the wrong document? No. It will all be explained—as long as you keep reading. I hope that you'll keep reading. Aside from a couple of changes, this is basically the same as the opening scenes of the Eleventh Hour. But this is basically the only thing that's canon compliant in this entire mess, so I had to establish it good and well first thing. Second thing that's probably running through your mind—how does he know her? Well, if you read the summary, I think that you can guess.**

**End game pairings for this story are for sure Doctor/Rose, and most likely Amy/Rory, but that one isn't one hundred percent certain right now. As it is, we won't be seeing Rory for awhile, so it'll be a bit complicated.**


	2. It Always Starts With Run

January 15th, 2005

Amy Pond kicked the curb nearest her mutinously. Okay, maybe London hadn't worked out how she had planned. She had the potential to make it as a model—she _knew _it. But nobody was willing to give a sixteen year old without any kind of a useful portfolio and no parental consent a shot. Seeing as her aunt was in Liverpool. Or Cardiff. Or not even in the UK anymore, for all that she knew.

She kept a modest flat in the bad part of town. Worked for a cafe as a hostess—shitty work, but all that a sixteen year old high school dropout who had run away to London to make it big could manage. Not that she had to pay for _everything_. Her aunt paid for the flat, sent her enough to cover living expenses—_barely_. The money from the job—every bit of it went towards her portfolio, her headshots.

But sometimes, no matter how hard she worked, it felt like she was just sitting on her arse, waiting for someone to come along and discover her. And that didn't sit well with Amelia Pond—she had ditched Leadworth at sixteen for a _reason_—she liked to be moving. The only thing worth staying in Leadworth for was Rory, but Rory had told her to go. It had broken his heart to do it, she knew, but he had told her to go, told her that he would join her in a few years, as soon as he had graduated and he could get the money for medical school.

Nobody else liked her in that crappy little town—the odd little girl with too-vibrant hair and too much of an imagination. She no longer believed in her own fantasies as she had when she was little. Maybe she really _had_ imagined the whole thing?

But the shed had been knocked down.

And what he had _said_. "I'll come for you when you're older, Amelia. Don't ever stop believing in me—please, don't ever stop believing in me. I won't look the same. I can change my face, and I won't look the same when you see me, but I'm still me."

She didn't believe it, even if the Raggedy Doctor _had_ been real. She didn't believe that she would ever see him again. And she _didn't_ believe that he could change his face.

She didn't believe, and she didn't hope, she tried to convince herself, _again_, for the fifth time today alone. For someone that she had met for an hour (if even) when she was seven, the Raggedy Doctor _still_ couldn't get out of her thoughts.

She decided that, since it was starting to get dark, moping in the streets right now was probably not the best plan. This was a nasty area of London, after all, and just because she knew some basic self defence (pull hair, bite and always go for the bullocks) didn't mean that it was smart to be loitering around at night, especially since she was a pretty young woman. Gorgeous, in fact, if she did say so herself. There was a reason why she had thought that she had real potential as a model, after all.

But then the yelling started, from two or three streets over, and she had always had an overdeveloped sense of adventure. She had to know what it was about. Despite the fact that there were several alleyway shortcuts that would get her there much faster, Amy was unwilling to take the risk of going through them now, when it was starting to get dark. She was still fast, though, and skirted up the nearest main street towards the source of the commotion.

It did not take her long to find it. A man in a leather jacket was hurtling towards her at top speed, yelling at the top of his lungs. And on his heels were several massively tall green things, bounding behind him like hunting dogs.

He hurtled up to her and grabbed her by the arm. "Come on, run!" He yelled, dragging her along for a bit before she got over the shock of the situation and started running under her own power.

"What _are_ those things?" She demanded of him, moving faster to put as much distance between the snapping teeth and her body as possible.

"Racans! From the planet Karlatan. Or, as you lot would probably put it, hellhounds," he yelled gleefully. He veered to the side, pulling her straight into one of the alleyways that she had been so determined to avoid. But it seemed to trick them, because they continued on straight.

"_What_?" Amy demanded, yanking her wrist away from him and bracing her hands on her knees to pant. Clearly, she wasn't in as great shape as she had thought that she was. Her pulse pounded in her temples.

"Racans," he repeated himself, more softly this time. "Or hellhounds. They're scent-tracking _something_, I just got in the way. And they'll eat anything that does that. You're lucky that I was here, else you would have gotten eaten."

"I _heard you_ the first time. Did you mean... like, aliens?"

"Yep!"

"Oh," Amy said weakly.

"Give it a minute," he offered. "Culture shock—happens to the best of us."

"I'm not shocked."

"I mean, not _me_, of course but—what do you mean, you aren't shocked?" He demanded. The expression—it was... familiar, somehow. She didn't know how—she'd never met this man before in her life. Or... she'd never _seen_ anyone who looked like him before in her life. But hadn't she _just_ been arguing with herself over the existence of a man who had claimed that he could change his face, who had _said_ that he would see her again. A man that had told her not to stop hoping?

"Doctor?" it slipped out before she could stop it, and she stepped forward to peer into his eyes.

"Yes? Do I know you?"

"I don't—I don't know what's happening," Amy said helplessly. "I don't understand _anything_. When I was seven, a blue police box crashed into my shed, and a man with a ripped up suit and floppy hair popped out, and he knew me. He knew who I was. And he told me that he could change his face, that I would see him again, because he'd come for me, but he'd look different. I still don't understand what happened."

"Interesting," the man said, peering at her carefully. He produced a fine metal tube and clicked it a few times, and the light at the end buzzed.

"He had that!" Amy said excitedly. "It _was_ you, wasn't it? You did do it? You _do_ exist! Everyone said that I was crazy!" She threw herself against him and hugged him tightly. He didn't seem to know what to do.

"I don't know," he said, pushing her away gently. Amy didn't let that discourage her. "I _am_ the Doctor, but it hasn't happened to me yet."

"What does _that_ mean?" Amy asked, wrinkling her nose.

"He didn't explain about time travel?" The Doctor asked exasperatedly.

"_Time travel_?" Amy repeated incredulously.

"Huh. Guess not," the Doctor said. "What's your name?"

"Amy. Amy Pond," Amy said.

"Amy Pond," he said, nodding. "Do you happen to know of someplace that I can get some quiet so that I can try to figure out what the hellhounds are tracking? They'll wreak devastation if they're left to roam London for long."

"Uhhm..." She was too smart to invite some man that was a complete stranger back to her flat—it would be a stupid thing to do, frankly. She might've been stupid enough to do it when she was seven, but she wasn't about to do it now. But... she was curious. About the time travel. And everything and... oh, maybe she should invite him back to her flat? He seemed mostly harmless. He hadn't hurt her when she was seven, after all.

"You live with your mum and dad?" He fished.

"No—ah, I live with my aunt," she lied. Stranger danger. She tried not to tell anyone that she lived alone in London. It wasn't like any proper guardian would have allowed it; her aunt was just a completely neglectful bitch who had never much cared for the responsibility of child-rearing, but had been too concerned for her reputation to allow her orphaned niece to be passed off into state care.

"There's a cafe, down that way," Amy offered. "I work there, it's still open."

"Sounds fantastic," he said, grinning infectiously at her. "Lead the way."

He followed her through the back alleyways without complaint—now that she had a male escort, she wasn't so worried about traversing those alleys after dark, and Amy led him to _Bella's_, the cafe that she worked at and pushed the door open to let him in.

It was mostly deserted—a single man in one corner, taking advantage of the free wireless internet access that they provided with a Cappuccino at his side. Mickey was the only person behind the counter, leaning against a barstool but not actually _sitting_ on it.

"Hey, red," Mickey said cheerfully as she came in. "Who's your friend?"

"Oh, just someone I met. He needed someplace to slow down for a minute."

"Fair enough. Mickey Smith," he said, offering a hand to shake. "Any friend of Amy's is a friend of mine. What can I get for you?"

"Coffee, please," the Doctor said. "Just milk. I'm the Doctor, by the way."

"Doctor who?" Mickey asked.

"Just the Doctor," he answered.

"What are you still doing here? Thought you weren't going to be around so much anymore—you said that you had picked up some more hours at the garage," Amy said, lifting up the middle partition and stepping behind the counter to help herself to the latte machine.

"Ah," Mickey said, wincing. "Needed some extra cash. Gran's hospital bills are getting bad again. What do you think you're doing, red?" He added playfully as Amy selected her mug from the cache of staff mugs (brought from home, so that they could have their own mug here) and added an assortment of flavourings and setting the milk to steam extra hot.

"Making my drink. Nobody else makes it right," Amy shot back.

"Yeah, and for good reason," Mickey said, snorting. "Who has hazelnut, caramel and _raspberry_ in the same latte?"

"It's good!" Amy mixed the milk, espresso, and expertly scooped a spoonful of foam onto her masterpiece, topping it off with a dollop of whipped cream and an excessive amount of caramel drizzle.

Mickey had prepared the Doctor's coffee, and waved off the offer of a couple of pound notes to pay for it. "Friend bonus," Mickey explained.

Amy led the Doctor to a table on the opposite side of the cafe from the other woman in the corner. "So. Time travel?"

"I'm a nine hundred year old time travelling alien with a time ship that's shaped like a blue police box, except she's bigger on the inside," the Doctor said, smirking. "When I'm dying, I regenerate into a new form. And, of course, the version of me that you met when you were seven had already met you now."

Amy gaped. "So that's how he—you—knew me?"

"Yes," the Doctor agreed. "And he likely only already knew that it would happen, because of what you're telling me now."

"So, which came first?"

He laughed. "I think I like you, Amy Pond. Most people would just gape at me when I mentioned time travel, but you ask me a technical question about time loops. And the answer is that I don't know. Perhaps I never would have told you the things that I told you if you hadn't just now told me—there's no point in getting into that," he interrupted himself.

Amy took a sip of her latte, thinking that maybe, she was going to need the caffeine.

**Here's the first real chapter! Nine meets his soon-to-be companion, Amelia Pond. As you could probably gather from the description of her childhood, Mels **_**was not**_** in it. There are reasons for this. River will come into play later, but it'll be a bit different from her role in canon. This Amy wanted out of Leadworth because of some different reasons—for one, I felt like Amy had spent her entire life waiting for the Doctor, and in this version, the Doctor didn't promise her five minutes. He said that he'd see her again, and if anything, she left town to look for him, at least subconsciously. She and Rory were best friends, but they never dated, partially because Mels wasn't there to push them together, and partially because she had been thinking of taking off for awhile, and therefore, she wasn't concentrating on relationships. I thought that the model thing was fairly realistic, partially because Karen Gillan was a model before she started acting, and partially because Amy was a model in Closing Time and The Asylum of the Daleks. Mickey probably won't play a huge role, but I just couldn't resist throwing him in there. Rose isn't around in this verse, and Mickey's not in love with Amy—they're just work friends, and that means that Mickey doesn't have a reason to feel the same sort of animosity towards the Doctor as he did in canon.**


	3. Following the Hounds of Hell

The Doctor had dug through a newspaper that had been left on the table, and managed to surface with a map of the London Underground. He explained patiently that whatever the hellhounds were looking for, it was underground, because they had been underground until they had been unable to get past the end of the line, and come out the top instead.

Hellhounds were apparently very stupid, even if they made good trackers. Which meant, of course, that they were working for someone. Someone had found and hired the hellhounds, and set them on the scent of the thing or person that they were searching for, which may be a good thing, or it may be a bad thing. The Doctor wasn't sure yet—he said that it depended on what they were looking for.

Amy just shrugged and finished her latte, chattering easily to fill up the silence. He didn't seem to talk all that much, and she had never been all that comfortable with silence—she had always had the urge to fill it, and when there wasn't anyone around to talk to, she talked to herself. Everyone at work was used to her aimless chatter by now, and Rory had used to pay attention to it with reverence.

And then—"A Macra egg!"

"Sorry?"

"There's a Macra egg in the London Underground! And if it hatches, it'll feed off of the steam and get bigger and bigger and more and more vicious. It'll start eating people—entire trains will just _go missing_."

"I still don't follow," Amy murmured. The Doctor set his coffee down on the table, grabbed her hand and hauled her to her feet.

"Come on!"

She left her mug on the table, waving apologetically to Mickey as the Doctor pulled her out the door.

"Where, exactly are we going?" Amy asked, eyeing him skeptically.

"The Underground, of course! Weren't you listening?"

"Listening, yes. Following, now," Amy muttered. He ignored her and set off down the street at top speed. "Doctor! Doctor!" She called.

He turned around and looked at her exasperatedly. "What _is _it, Amy Pond?"

"The nearest entrance to the Underground is that way," she said, pointing in the opposite direction.

"Oh," he said, making a face. "I knew that."

"Sure you did," Amy said sarcastically as he wheeled around to start back the way that he had come, grabbing her arm and pulling her with him along the way.

There were three blocks between them and the London Underground, and the Doctor insisted on dragging her across them fast enough that her elbow nearly caved in backwards.

He ran down the stairs and leapt over the turnstile, and Amy winced and followed him, hoping that there weren't security cameras down here. Then he reached the train platform, looked both ways and, after establishing that there weren't any trains on the tracks, hopped into the train tracks.

"What are you _doing_?" Amy shrieked.

"What did you think, that the potentially dangerous egg of a nearly extinct species is sitting on a train platform? Not likely! It's in there." He held his hand up in her direction. "Want to come with me?"

"Goddamnit, who _are _you?" She demanded. He looked at her and boosted himself back up beside her. Then he reached forward and cautiously took her hand and time seemed to slow to a stop. There was nothing except for her not-so-Raggedy Doctor and her, standing in the London Underground.

"You know when you were a kid? And they told you that the earth was moving, and you couldn't quite believe it because everything looked like it was standing still? I can feel it. I can feel the earth spinning at 1000 miles per hour, and moving around the sun at 67, 000 miles per hour. We're falling through space, you and me, _clinging _to the skin of this tiny little world, and if we let go—" He dropped her hand, and time started again. "That's it. That's who I am. And I'd tell you to forget me, but I think that, thanks to my older self, that isn't going to happen."

"No," Amy admitted.

"So." He stepped forward, looked into her eyes. "You've seen my ship. She was probably a little bit worse for wear, the first time that you met her, but you've seen her. Want to come with me? Want to come and see the universe? All of time and space, where do you want to go?"

What did she _have_ here, anyway? The vague promise that Rory would come and join her in London once he had graduated and managed to save enough money for medical school? An aunt that didn't even bother to tell her what part of the world she was in? "Yes," she said, without entirely giving her mouth permission to say the word. "Yes, I want to see everything."

"Good. Come on, then."

And, not allowing herself to question her sanity, she followed him into the train tunnel without looking back.

...

What was he _doing_? Why was he inviting her along? Sure, she was a plucky ginger, and sure, she had met his future-self—a sure sign that he could trust her—but why would he invite her along? He didn't _deserve_ companions. People who destroyed their entire species in a storm of fire and blood did not get to travel the universe with a hand to hold. He wasn't allowed to die in the war—that would have been too kind—and now it was his penance to travel on alone.

Plus, the things that happened to his companions—Amy Pond deserved better than that. Amy Pond deserved better than to lose her memories like Jamie, or be left behind like Sarah Jane, or to _die_ like Adric.

He loved them all, but it was his penance to never see them again, and to lose them forever, and to never again ruin a life like he had in the past.

He had been resolved to that—he had stopped an invasion of the Living Plastic just a few... well, a few months _from now_, if he was honest, and he could have picked up that girl, Shareen (the one that he had rescued from a basement department store), but he _didn't_. Because he didn't deserve the companionship, and a little platinum blonde from twenty-first century London didn't deserve to have her life destroyed by a lonely and angry old man who trailed war and death in his wake.

And neither did Amy Pond. Plus, she was a _kid_, sixteen years old, probably. He hadn't asked, but she couldn't have been much older than that. Beautiful, for certain, but in a fresh, untouched, innocent sort of way.

"So," she said, glancing at him as he led her into a dark tunnel. "Do you have any idea where you're going?"

"Not a clue," the Doctor said cheerfully. "You?"

She quirked her lips at him. "Nope," she said.

"Isn't it wonderful?"

She rolled her eyes at him. "I like to know where I'm going," she said. "I never watch a movie without seeing the trailer first. I never go anywhere without looking at a map."

"Oh! You ruin it," he said dramatically.

"I'm a small town girl alone in London—it takes planning, you know."

"Alone? I thought you lived with your aunt?"

"I lied. What, was I supposed to tell you that I lived alone? You could've been a serial killer," she said. "My aunt doesn't care enough about me to live with me. She didn't bother in Leadworth when I was seven, and she hasn't bothered now. She pays the bills, and she leaves me to my own devices. Rather than having to actually _pay attention_ to her orphaned niece," Amy scoffed bitterly.

"If I'm a serial killer, you've probably been very stupid, following me down a dark tunnel," he pointed out.

"Eh," Amy shrugged. "You've convinced me of your trustworthiness—ah!" And, of course, because nothing in his life could possibly be _easy_, there was a train coming right at them. He grabbed her and pulled her into the slight hallway leading to a service door, and flattened them both against the wall. The train whipped by, and Amy could feel the air on her skin.

"Jesus Christ," she muttered. "You like to cut it close, don't you?"

"Little bit," he agreed. Must not let her see. He couldn't stop and think about the consequences the last time that he had _cut it close_, when he had finally listened to Romana's horrible, terrible last request. "Tell me, why do you _really_ plan everything?"

"Because Rory told me to," Amy said.

"Who's Rory? Boyfriend?" He had the irrepressible urge to hunt down this _Rory_ and inform him that if he broke Amy's heart, he would be answering to the Oncoming Storm.

"Ehem," Amy evaded. "Uhm... I—no. I mean, Rory—he's always been there for me, but I don't think that he's interested?" The Doctor eyed her sceptically. Legs like that, what teenage boy _wouldn't_ be interested? "He's gay," Amy said flatly.

"Are you sure?" the Doctor said doubtfully.

"Very. We've been friends for eight years, and he's _never_ shown an interest in a girl."

"He ever _told you_ that he was gay? Shown interest in boys instead?"

"Wellllll. No. But I always figured that he would tell me when he was ready, right? I... I guess I would be interested, if he was. But I've never really thought about it. Because Rory's gay." She nodded firmly, and the Doctor let it go. He didn't know Rory, and he couldn't know one way or the other if Rory was gay.

The steam was getting thicker. Amy was coughing intermittently, and he cursed himself for not realizing that she did not have a respitory bypass, and that she wouldn't be able to breathe properly through all of the smoke that a Macra egg would inevitably attract.

But, it meant that they were getting closer. And apparently, they had failed to beat the hellhounds here. Fantastic.

Amy dove to one side and kicked the hellhound that tried to leap onto her. The Doctor was very proud of how quickly she had adapted to being attacked. That probably wasn't a _good_ thing, but he got attacked a lot. Unfortunate, but true.

Typical hellhound, it got bored of the person that wasn't its prey, and moved forward into the smog. The Doctor pulled Amy to her feet and followed it. If someone was benevolently trying to get the Macra egg out of here before it pulled the underground apart, then he would be content. But if they were willing to send hellhounds after it, then the clearly didn't much care about collateral damage, which wasn't all that comforting. Which meant that he needed to get to the egg first, and he would drop it off on some deserted smog planet, where it could hatch and eat smoke in peace. Then he'd send the hellhounds back to mummy and daddy, and figure out what mummy/daddy had planned for that Macra egg, and whether they'd be a problem in the future.

Easy. No problem. And the whole bit about having a new companion in tow... well, maybe that was slightly more complicated, but he'd manage it. He was the Doctor—he always did.

**Here's another update—three chapters in three days, I doubt that speed'll keep up, no matter how hard that I try. But I will do my best. Not much actually **_**happened**_** in this chapter, except that now they're poised to run into danger, and, despite his every instinct screaming him away from it, Nine's invited Amy to go travelling with him. **


End file.
